Research workbench
Crystal structure of the R463A mutant of human glutamate dehydrogenase
Analyse Crystal structure of the R463A mutant of human glutamate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NR1
- Type
- protein
- Length
- 2,976 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase 1
- EC
- 1.4.1.3
- UniProt
- P00367
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate dehydrogenase 1 (EC 1.4.1.3) | protein | 496 | 49% helix, 12% strand | P00367 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.90 | 0.93 | 130 | empty |
| 2 | 897 | 0.90 | 0.93 | 113 | empty |
| 3 | 824 | 0.88 | 0.90 | 48 | empty |
| 4 | 861 | 0.88 | 0.90 | 49 | empty |
| 5 | 495 | 0.86 | 0.93 | 56 | empty |
Interfaces
15 interfaces between chains.
- D–E · 1798 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 1763 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1759 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1755 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 1746 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1NR1 · Crystal structure of the R463A mutant of human Glutamate dehydrogenase · the same entry in another collection · chain F against F, TM-score 1.00
- P00367 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase 1, mitochondrial (P00367) · a predicted model of the same protein · chain B against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00367
- Elsewhere: RCSB PDB 1NR1 · PDBe 1NR1 · UniProt P00367
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